Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
24.5 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.42, Jaccard 0.28
Reason: 8 internal clashes
8 intramolecular clashes
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.920 kcal/mol/HA)
✓ Good fit quality (FQ -8.48)
✓ Good H-bonds (4 bonds)
✓ Good burial (57% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-23.933
kcal/mol
LE
-0.920
kcal/mol/HA
Fit Quality
-8.48
FQ (Leeson)
HAC
26
heavy atoms
MW
355
Da
LogP
2.55
cLogP
Interaction summary
HB 4
HY 17
PI 0
CLASH 0
⚠ Exposure 36%
Interaction summary
HB 4
HY 17
PI 0
CLASH 0
⚠ Exposure 36%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 12
Exposed 7
LogP 2.55
H-bonds 4
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.929 | Score | -23.933 |
|---|---|---|---|
| Inter norm | -0.921 | Intra norm | 0.001 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes; moderate strain Δ 24.5 | ||
| Residues |
ALA90
ASN91
GLY214
LYS211
LYS89
PRO187
PRO212
PRO213
TRP92
TYR210
VAL88
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 5 | Native recall | 0.42 |
| Jaccard | 0.28 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 475 | -0.08221971147585513 | -1.22415 | -30.2593 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 477 | 1.8981738757489897 | -0.909646 | -18.3539 | 6 | 9 | 0 | 0.00 | - | - | no | Open |
| 471 | 2.0914954337275034 | -0.968051 | -23.7617 | 6 | 13 | 0 | 0.00 | - | - | no | Open |
| 533 | 3.9293307203846424 | -0.921293 | -23.9335 | 4 | 11 | 5 | 0.42 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.933kcal/mol
Ligand efficiency (LE)
-0.9205kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.481
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
355.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.55
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-152.54kcal/mol
Minimised FF energy
-177.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
663.5Ų
Total solvent-accessible surface area of free ligand
BSA total
375.9Ų
Buried surface area upon binding
BSA apolar
325.2Ų
Hydrophobic contacts buried
BSA polar
50.7Ų
Polar contacts buried
Fraction buried
56.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3200.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1473.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)